As time went by, and Zelda and Mario mania died down, interest in the Zelda series dwindled. This changed in April 1992 with the release of the first Zelda game in four years, this time on the Super Nintendo Entertainment System. This game went back to the overhead view and gameplay of the original Legend of Zelda, and introduced the Light World and Dark World.

The instruction booklet tells of the creation of Hyrule by three golden gods, and the accidental discovery of the Triforce by Ganondorf Dragmire, King of Thieves, while Hyrule was engulfed in war. Soon evil streamed into Hyrule from the tainted Golden Land, and Ganondorf became known as Mandrag Ganon. Ganon's army attacked Hyrule Castle, and the Knights of Hyrule bought time for the Seven Wise Men to seal Ganon, the King of Evil. This battle later became known as the Imprisoning War, and the world Ganon created in place of the Golden Land became known as the Dark World.

Centuries later, a wizard named Agahnim has stopped disasters that have beset Hyrule recently. The King has made him advisor to the throne and heir to the Seven Wise Men, but Agahnim is actually Ganon's pawn. Agahnim has secretly taken the place of the King, and kidnapped all the descendants of the Seven Wise Men. Late at night he is sending them into the Dark World, to help break the Seven Wise Men's Seal and free Ganon. When Princess Zelda is sent into the Dark World, the seal of the Seven Wise Men will be broken.

Princess Zelda is being held in the dungeon of Hyrule Castle, and the time has almost come for her, the last descendant, to be sent into the Dark World. But Zelda contacts Link telepathically, begging for his help. Link is living with his uncle, and the game begins on a stormy night as both Link and his uncle hear Zelda's plea. Link's uncle rushes to the castle with sword and shield, telling Link to stay in bed. But Link soon follows after him, concerned for both Zelda and his uncle.

Link must retrieve three Pendants of Virtue to get the Master Sword and defeat Agahnim. He must also save six maidens and Princess Zelda from the Dark World, and defeat Ganon to prevent him from entering Hyrule once more.